GAF file QC
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(Created page with 'The following quality control checks should be performed before submitting a GAF file to the Gene Ontology Consortium. Remove any duplicate lines in the file (this can be easily…') |
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Ensure all external entities referenced in the file (e.g. in the '''with/from''' column) use the correct database prefix, as specified in the [http://www.geneontology.org/doc/GO.xrf_abbs xref abbreviations file] | Ensure all external entities referenced in the file (e.g. in the '''with/from''' column) use the correct database prefix, as specified in the [http://www.geneontology.org/doc/GO.xrf_abbs xref abbreviations file] | ||
| + | |||
| + | Check GAF based on taxon constraints - see [[GAF_Taxonomy_Reasoning]] for details. This can be done in two ways | ||
| + | * Submit the GAF and then check the report some time later | ||
| + | * Install the GOBO package and run the constraints locally prior to submission | ||
| + | |||
| + | The first way is certainly easier, but the disadvantage is that the gaffes are public for a while. The second will require the help of someone experienced with installing perl modules. | ||
[[Category:Annotation]] | [[Category:Annotation]] | ||
[[Category:GAF]] | [[Category:GAF]] | ||
Latest revision as of 20:09, 8 January 2010
The following quality control checks should be performed before submitting a GAF file to the Gene Ontology Consortium.
Remove any duplicate lines in the file (this can be easily accomplished by performing sort -u on Unix)
Ensure all external entities referenced in the file (e.g. in the with/from column) use the correct database prefix, as specified in the xref abbreviations file
Check GAF based on taxon constraints - see GAF_Taxonomy_Reasoning for details. This can be done in two ways
- Submit the GAF and then check the report some time later
- Install the GOBO package and run the constraints locally prior to submission
The first way is certainly easier, but the disadvantage is that the gaffes are public for a while. The second will require the help of someone experienced with installing perl modules.
